[BioC] Two rma questions

[James MacDonald]

For your first question, it is almost always preferable to run rma on
all samples in a set together rather than in two batches. For the second
question, the bug only concerns justRMA and justGCRMA, so rma and gcrma
are not affected.

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Simon Kidd <kidd at mail.rockefeller.edu> 04/14/04 11:35AM >>>
Hi,

We have been comparing the effects of a mutation to two different 
duplications of the wild type gene (ie  g-  v g-/dp1(g+)  and g-  v 
g-/dp2(g+)) and then doing rma on either the pooled affy chips or the 
two genotypes separately and then pooling them for analysis in dChip. 
But which of the methods, separate or together is the statistically 
the correct way of doing the rma analysis? The two give different 
numbers of differentially expressed genes.

The second question, does rma  in affy v1.4.21 have the same bug as 
justRMA and gcRMA in affy v1.4.22?

thanks,

Simon

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